/** Gets the distances between the source and detectors whose IDs you pass to it
* @param WS :: the input workspace
* @param mon0Spec :: Spectrum number of the output from the first monitor
* @param mon1Spec :: Spectrum number of the output from the second monitor
* @param monitor0Dist :: the calculated distance to the detector whose ID was
* passed to this function first
* @param monitor1Dist :: calculated distance to the detector whose ID was
* passed to this function second
* @throw NotFoundError if no detector is found for the detector ID given
*/
void GetEi::getGeometry(API::MatrixWorkspace_const_sptr WS, specid_t mon0Spec,
specid_t mon1Spec, double &monitor0Dist,
double &monitor1Dist) const {
const IComponent_const_sptr source = WS->getInstrument()->getSource();
// retrieve a pointer to the first detector and get its distance
size_t monWI = 0;
try {
monWI = WS->getIndexFromSpectrumNumber(mon0Spec);
} catch (std::runtime_error &) {
g_log.error()
<< "Could not find the workspace index for the monitor at spectrum "
<< mon0Spec << "\n";
g_log.error() << "Error retrieving data for the first monitor" << std::endl;
throw std::bad_cast();
}
const std::set<detid_t> &dets = WS->getSpectrum(monWI)->getDetectorIDs();
if (dets.size() != 1) {
g_log.error() << "The detector for spectrum number " << mon0Spec
<< " was either not found or is a group, grouped monitors "
"are not supported by this algorithm\n";
g_log.error() << "Error retrieving data for the first monitor" << std::endl;
throw std::bad_cast();
}
IDetector_const_sptr det = WS->getInstrument()->getDetector(*dets.begin());
monitor0Dist = det->getDistance(*(source.get()));
// repeat for the second detector
try {
monWI = WS->getIndexFromSpectrumNumber(mon0Spec);
} catch (std::runtime_error &) {
g_log.error()
<< "Could not find the workspace index for the monitor at spectrum "
<< mon0Spec << "\n";
g_log.error() << "Error retrieving data for the second monitor\n";
throw std::bad_cast();
}
const std::set<detid_t> &dets2 = WS->getSpectrum(monWI)->getDetectorIDs();
if (dets2.size() != 1) {
g_log.error() << "The detector for spectrum number " << mon1Spec
<< " was either not found or is a group, grouped monitors "
"are not supported by this algorithm\n";
g_log.error() << "Error retrieving data for the second monitor\n";
throw std::bad_cast();
}
det = WS->getInstrument()->getDetector(*dets2.begin());
monitor1Dist = det->getDistance(*(source.get()));
}
/** Checks that the two input workspaces have non-overlapping spectra numbers and contributing detectors
* @param ws1 :: The first input workspace
* @param ws2 :: The second input workspace
* @param checkSpectra :: set to true to check for overlapping spectra numbers (non-sensical for event workspaces)
* @throw std::invalid_argument If there is some overlap
*/
void ConjoinWorkspaces::checkForOverlap(API::MatrixWorkspace_const_sptr ws1, API::MatrixWorkspace_const_sptr ws2, bool checkSpectra) const
{
// make sure we should bother checking
if (!this->getProperty("CheckOverlapping"))
return;
// Loop through the first workspace adding all the spectrum numbers & UDETS to a set
std::set<specid_t> spectra;
std::set<detid_t> detectors;
const size_t& nhist1 = ws1->getNumberHistograms();
for (size_t i = 0; i < nhist1; ++i)
{
const ISpectrum * spec = ws1->getSpectrum(i);
const specid_t spectrum = spec->getSpectrumNo();
spectra.insert(spectrum);
const std::set<detid_t> & dets = spec->getDetectorIDs();
std::set<detid_t>::const_iterator it;
for (it = dets.begin(); it != dets.end(); ++it)
{
detectors.insert(*it);
}
}
// Now go throught the spectrum numbers & UDETS in the 2nd workspace, making sure that there's no overlap
const size_t& nhist2 = ws2->getNumberHistograms();
for (size_t j = 0; j < nhist2; ++j)
{
const ISpectrum * spec = ws2->getSpectrum(j);
const specid_t spectrum = spec->getSpectrumNo();
if (checkSpectra)
{
if ( spectrum > 0 && spectra.find(spectrum) != spectra.end() )
{
g_log.error("The input workspaces have overlapping spectrum numbers");
throw std::invalid_argument("The input workspaces have overlapping spectrum numbers");
}
}
const std::set<detid_t> & dets = spec->getDetectorIDs();
std::set<detid_t>::const_iterator it;
for (it = dets.begin(); it != dets.end(); ++it)
{
if ( detectors.find(*it) != detectors.end() )
{
g_log.error("The input workspaces have common detectors");
throw std::invalid_argument("The input workspaces have common detectors");
}
}
}
}
/** Checks that the two input workspaces have non-overlapping spectra numbers
* and contributing detectors
* @param ws1 :: The first input workspace
* @param ws2 :: The second input workspace
* @param checkSpectra :: set to true to check for overlapping spectra numbers
* (non-sensical for event workspaces)
* @throw std::invalid_argument If there is some overlap
*/
void ConjoinWorkspaces::checkForOverlap(API::MatrixWorkspace_const_sptr ws1,
API::MatrixWorkspace_const_sptr ws2,
bool checkSpectra) const {
// Loop through the first workspace adding all the spectrum numbers & UDETS to
// a set
std::set<specnum_t> spectra;
std::set<detid_t> detectors;
const size_t &nhist1 = ws1->getNumberHistograms();
for (size_t i = 0; i < nhist1; ++i) {
const ISpectrum *spec = ws1->getSpectrum(i);
const specnum_t spectrum = spec->getSpectrumNo();
spectra.insert(spectrum);
const auto &dets = spec->getDetectorIDs();
for (auto const &det : dets) {
detectors.insert(det);
}
}
// Now go throught the spectrum numbers & UDETS in the 2nd workspace, making
// sure that there's no overlap
const size_t &nhist2 = ws2->getNumberHistograms();
for (size_t j = 0; j < nhist2; ++j) {
const ISpectrum *spec = ws2->getSpectrum(j);
const specnum_t spectrum = spec->getSpectrumNo();
if (checkSpectra) {
if (spectrum > 0 && spectra.find(spectrum) != spectra.end()) {
g_log.error()
<< "The input workspaces have overlapping spectrum numbers "
<< spectrum << "\n";
throw std::invalid_argument(
"The input workspaces have overlapping spectrum numbers");
}
}
const auto &dets = spec->getDetectorIDs();
for (const auto &det : dets) {
if (detectors.find(det) != detectors.end()) {
g_log.error() << "The input workspaces have common detectors: " << (det)
<< "\n";
throw std::invalid_argument(
"The input workspaces have common detectors");
}
}
}
}
/**
* Only to be used if the KeepUnGrouped property is true, moves the spectra that were not selected
* to be in a group to the end of the output spectrum
* @param unGroupedSet :: list of WORKSPACE indexes that were included in a group
* @param inputWS :: user selected input workspace for the algorithm
* @param outputWS :: user selected output workspace for the algorithm
* @param outIndex :: the next spectra index available after the grouped spectra
*/
void GroupDetectors2::moveOthers(const std::set<int64_t> &unGroupedSet, API::MatrixWorkspace_const_sptr inputWS, API::MatrixWorkspace_sptr outputWS,
size_t outIndex)
{
g_log.debug() << "Starting to copy the ungrouped spectra" << std::endl;
double prog4Copy = (1. - 1.*static_cast<double>(m_FracCompl))/static_cast<double>(unGroupedSet.size());
std::set<int64_t>::const_iterator copyFrIt = unGroupedSet.begin();
// go thorugh all the spectra in the input workspace
for ( ; copyFrIt != unGroupedSet.end(); ++copyFrIt )
{
if( *copyFrIt == USED ) continue; //Marked as not to be used
size_t sourceIndex = static_cast<size_t>(*copyFrIt);
// The input spectrum we'll copy
const ISpectrum * inputSpec = inputWS->getSpectrum(sourceIndex);
// Destination of the copying
ISpectrum * outputSpec = outputWS->getSpectrum(outIndex);
// Copy the data
outputSpec->dataX() = inputSpec->dataX();
outputSpec->dataY() = inputSpec->dataY();
outputSpec->dataE() = inputSpec->dataE();
// Spectrum numbers etc.
outputSpec->setSpectrumNo(inputSpec->getSpectrumNo());
outputSpec->clearDetectorIDs();
outputSpec->addDetectorIDs( inputSpec->getDetectorIDs() );
// go to the next free index in the output workspace
outIndex ++;
// make regular progress reports and check for cancelling the algorithm
if ( outIndex % INTERVAL == 0 )
{
m_FracCompl += INTERVAL*prog4Copy;
if ( m_FracCompl > 1.0 )
{
m_FracCompl = 1.0;
}
progress(m_FracCompl);
interruption_point();
}
}
// Refresh the spectraDetectorMap
outputWS->generateSpectraMap();
g_log.debug() << name() << " copied " << unGroupedSet.size()-1 << " ungrouped spectra\n";
}
/**
* If the InstrumentParameter property is set then it attempts to retrieve the parameter
* from the component, else it returns the value of the Factor property
* @param inputWS A pointer to the input workspace
* @param index The current index to inspect
* @return Value for the scale factor
*/
double ScaleX::getScaleFactor(const API::MatrixWorkspace_const_sptr & inputWS, const size_t index)
{
if(m_parname.empty()) return m_algFactor;
// Try and get factor from component. If we see a DetectorGroup use this will use the first component
Geometry::IDetector_const_sptr det;
auto inst = inputWS->getInstrument();
auto *spec = inputWS->getSpectrum(index);
const auto & ids = spec->getDetectorIDs();
const size_t ndets(ids.size());
if(ndets > 0)
{
try
{
det = inst->getDetector(*ids.begin());
}
catch(Exception::NotFoundError&)
{
return 0.0;
}
}
else return 0.0;
const auto & pmap = inputWS->constInstrumentParameters();
auto par = pmap.getRecursive(det->getComponentID(), m_parname);
if(par)
{
if(!m_combine) return par->value<double>();
else return m_binOp(m_algFactor,par->value<double>());
}
else
{
std::ostringstream os;
os << "Spectrum at index '" << index << "' has no parameter named '" << m_parname << "'\n";
throw std::runtime_error(os.str());
}
}
/**
* Move the user selected spectra in the input workspace into groups in the output workspace
* @param inputWS :: user selected input workspace for the algorithm
* @param outputWS :: user selected output workspace for the algorithm
* @param prog4Copy :: the amount of algorithm progress to attribute to moving a single spectra
* @return number of new grouped spectra
*/
size_t GroupDetectors2::formGroups( API::MatrixWorkspace_const_sptr inputWS, API::MatrixWorkspace_sptr outputWS,
const double prog4Copy)
{
// get "Behaviour" string
const std::string behaviour = getProperty("Behaviour");
int bhv = 0;
if ( behaviour == "Average" ) bhv = 1;
API::MatrixWorkspace_sptr beh = API::WorkspaceFactory::Instance().create(
"Workspace2D", static_cast<int>(m_GroupSpecInds.size()), 1, 1);
g_log.debug() << name() << ": Preparing to group spectra into " << m_GroupSpecInds.size() << " groups\n";
// where we are copying spectra to, we start copying to the start of the output workspace
size_t outIndex = 0;
// Only used for averaging behaviour. We may have a 1:1 map where a Divide would be waste as it would be just dividing by 1
bool requireDivide(false);
for ( storage_map::const_iterator it = m_GroupSpecInds.begin(); it != m_GroupSpecInds.end() ; ++it )
{
// This is the grouped spectrum
ISpectrum * outSpec = outputWS->getSpectrum(outIndex);
// The spectrum number of the group is the key
outSpec->setSpectrumNo(it->first);
// Start fresh with no detector IDs
outSpec->clearDetectorIDs();
// Copy over X data from first spectrum, the bin boundaries for all spectra are assumed to be the same here
outSpec->dataX() = inputWS->readX(0);
// the Y values and errors from spectra being grouped are combined in the output spectrum
// Keep track of number of detectors required for masking
size_t nonMaskedSpectra(0);
beh->dataX(outIndex)[0] = 0.0;
beh->dataE(outIndex)[0] = 0.0;
for( std::vector<size_t>::const_iterator wsIter = it->second.begin(); wsIter != it->second.end(); ++wsIter)
{
const size_t originalWI = *wsIter;
// detectors to add to firstSpecNum
const ISpectrum * fromSpectrum = inputWS->getSpectrum(originalWI);
// Add up all the Y spectra and store the result in the first one
// Need to keep the next 3 lines inside loop for now until ManagedWorkspace mru-list works properly
MantidVec &firstY = outSpec->dataY();
MantidVec::iterator fYit;
MantidVec::iterator fEit = outSpec->dataE().begin();
MantidVec::const_iterator Yit = fromSpectrum->dataY().begin();
MantidVec::const_iterator Eit = fromSpectrum->dataE().begin();
for (fYit = firstY.begin(); fYit != firstY.end(); ++fYit, ++fEit, ++Yit, ++Eit)
{
*fYit += *Yit;
// Assume 'normal' (i.e. Gaussian) combination of errors
*fEit = std::sqrt( (*fEit)*(*fEit) + (*Eit)*(*Eit) );
}
// detectors to add to the output spectrum
outSpec->addDetectorIDs(fromSpectrum->getDetectorIDs() );
try
{
Geometry::IDetector_const_sptr det = inputWS->getDetector(originalWI);
if( !det->isMasked() ) ++nonMaskedSpectra;
}
catch(Exception::NotFoundError&)
{
// If a detector cannot be found, it cannot be masked
++nonMaskedSpectra;
}
}
if( nonMaskedSpectra == 0 ) ++nonMaskedSpectra; // Avoid possible divide by zero
if(!requireDivide) requireDivide = (nonMaskedSpectra > 1);
beh->dataY(outIndex)[0] = static_cast<double>(nonMaskedSpectra);
// make regular progress reports and check for cancelling the algorithm
if ( outIndex % INTERVAL == 0 )
{
m_FracCompl += INTERVAL*prog4Copy;
if ( m_FracCompl > 1.0 )
m_FracCompl = 1.0;
progress(m_FracCompl);
interruption_point();
}
outIndex ++;
}
// Refresh the spectraDetectorMap
outputWS->generateSpectraMap();
if ( bhv == 1 && requireDivide )
{
g_log.debug() << "Running Divide algorithm to perform averaging.\n";
Mantid::API::IAlgorithm_sptr divide = createChildAlgorithm("Divide");
divide->initialize();
divide->setProperty<API::MatrixWorkspace_sptr>("LHSWorkspace", outputWS);
divide->setProperty<API::MatrixWorkspace_sptr>("RHSWorkspace", beh);
divide->setProperty<API::MatrixWorkspace_sptr>("OutputWorkspace", outputWS);
divide->execute();
}
g_log.debug() << name() << " created " << outIndex << " new grouped spectra\n";
return outIndex;
}
/**
* Function that retrieves the two-theta and azimuthal angles from a given
* detector. It then looks up the nearest neighbours. Using those detectors,
* it calculates the two-theta and azimuthal angle widths.
* @param workspace : the workspace containing the needed detector information
*/
void SofQW3::getValuesAndWidths(API::MatrixWorkspace_const_sptr workspace)
{
// Trigger a build of the nearst neighbors outside the OpenMP loop
const int numNeighbours = 4;
const size_t nHistos = workspace->getNumberHistograms();
g_log.debug() << "Number of Histograms: " << nHistos << std::endl;
this->m_theta = std::vector<double>(nHistos);
this->m_thetaWidths = std::vector<double>(nHistos);
this->m_phi = std::vector<double>(nHistos);
this->m_phiWidths = std::vector<double>(nHistos);
for (size_t i = 0; i < nHistos; ++i)
{
m_progress->report("Calculating detector angular widths");
DetConstPtr detector = workspace->getDetector(i);
g_log.debug() << "Current histogram: " << i << std::endl;
specid_t inSpec = workspace->getSpectrum(i)->getSpectrumNo();
SpectraDistanceMap neighbours = workspace->getNeighboursExact(inSpec,
numNeighbours,
true);
g_log.debug() << "Current ID: " << inSpec << std::endl;
// Convert from spectrum numbers to workspace indices
double thetaWidth = -DBL_MAX;
double phiWidth = -DBL_MAX;
// Find theta and phi widths
double theta = workspace->detectorTwoTheta(detector);
double phi = detector->getPhi();
specid_t deltaPlus1 = inSpec + 1;
specid_t deltaMinus1 = inSpec - 1;
specid_t deltaPlusT = inSpec + this->m_detNeighbourOffset;
specid_t deltaMinusT = inSpec - this->m_detNeighbourOffset;
for (SpectraDistanceMap::iterator it = neighbours.begin();
it != neighbours.end(); ++it)
{
specid_t spec = it->first;
g_log.debug() << "Neighbor ID: " << spec << std::endl;
if (spec == deltaPlus1 || spec == deltaMinus1 ||
spec == deltaPlusT || spec == deltaMinusT)
{
DetConstPtr detector_n = workspace->getDetector(spec - 1);
double theta_n = workspace->detectorTwoTheta(detector_n);
double phi_n = detector_n->getPhi();
double dTheta = std::fabs(theta - theta_n);
double dPhi = std::fabs(phi - phi_n);
if (dTheta > thetaWidth)
{
thetaWidth = dTheta;
//g_log.debug() << "Current ThetaWidth: " << thetaWidth << std::endl;
}
if (dPhi > phiWidth)
{
phiWidth = dPhi;
//g_log.debug() << "Current PhiWidth: " << phiWidth << std::endl;
}
}
}
this->m_theta[i] = theta;
this->m_phi[i] = phi;
this->m_thetaWidths[i] = thetaWidth;
this->m_phiWidths[i] = phiWidth;
}
}
/**
* Apply the detector test criterion
* @param counts1 :: A workspace containing the integrated counts of the first
* white beam run
* @param counts2 :: A workspace containing the integrated counts of the first
* white beam run
* @param average :: The computed median
* @param variation :: The allowed variation in terms of number of medians, i.e
* those spectra where
* the ratio of the counts outside this range will fail the tests and will be
* masked on counts1
* @return number of detectors for which tests failed
*/
int DetectorEfficiencyVariation::doDetectorTests(
API::MatrixWorkspace_const_sptr counts1,
API::MatrixWorkspace_const_sptr counts2, const double average,
double variation) {
// DIAG in libISIS did this. A variation of less than 1 doesn't make sense in
// this algorithm
if (variation < 1) {
variation = 1.0 / variation;
}
// criterion for if the the first spectrum is larger than expected
double largest = average * variation;
// criterion for if the the first spectrum is lower than expected
double lowest = average / variation;
const int numSpec = static_cast<int>(counts1->getNumberHistograms());
const int progStep = static_cast<int>(std::ceil(numSpec / 30.0));
// Create a workspace for the output
MaskWorkspace_sptr maskWS = this->generateEmptyMask(counts1);
bool checkForMask = false;
Geometry::Instrument_const_sptr instrument = counts1->getInstrument();
if (instrument != nullptr) {
checkForMask = ((instrument->getSource() != nullptr) &&
(instrument->getSample() != nullptr));
}
const double deadValue(1.0);
int numFailed(0);
PARALLEL_FOR3(counts1, counts2, maskWS)
for (int i = 0; i < numSpec; ++i) {
PARALLEL_START_INTERUPT_REGION
// move progress bar
if (i % progStep == 0) {
advanceProgress(progStep * static_cast<double>(RTMarkDetects) / numSpec);
progress(m_fracDone);
interruption_point();
}
if (checkForMask) {
const std::set<detid_t> &detids =
counts1->getSpectrum(i)->getDetectorIDs();
if (instrument->isMonitor(detids))
continue;
if (instrument->isDetectorMasked(detids)) {
// Ensure it is masked on the output
maskWS->dataY(i)[0] = deadValue;
continue;
}
}
const double signal1 = counts1->readY(i)[0];
const double signal2 = counts2->readY(i)[0];
// Mask out NaN and infinite
if (boost::math::isinf(signal1) || boost::math::isnan(signal1) ||
boost::math::isinf(signal2) || boost::math::isnan(signal2)) {
maskWS->dataY(i)[0] = deadValue;
PARALLEL_ATOMIC
++numFailed;
continue;
}
// Check the ratio is within the given range
const double ratio = signal1 / signal2;
if (ratio < lowest || ratio > largest) {
maskWS->dataY(i)[0] = deadValue;
PARALLEL_ATOMIC
++numFailed;
}
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
// Register the results with the ADS
setProperty("OutputWorkspace", maskWS);
return numFailed;
}